I suggest you use ChimeraX. We have not developed Chimera for a long time and ChimeraX does all this map stuff and we are more likely to answer questions about ChimeraX. Tom
On Dec 9, 2021, at 10:55 AM, Elaine Meng via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Si Hoon Park, That's a lot of questions! I will try to number them separately.
(1) Chimera can read some IMOD file types. Here is the list of the file types Chimera can read: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html>
In the volume (density-map) category, IMOD map: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume>
In the 3D object category, IMOD segmentation: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#object> ... as further described here: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/imod...>
(2) Chimera also has many options for map filtering and masking. See the "volume guide" <https://www.rbvi.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html>
...and specific documentation for many Volume-related tools (menu: Tools... Volume Data... Volume Viewer and others), commands "volume" "vop" and "mask" and others: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/fram...> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volu...> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html>
(3) You can hand-draw in Chimera by putting markers on slices with Volume Tracer and then combining the markers to make surfaces (also using that same tool). <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/...> However, this is very labor-intensive and if you already have a surface created by some other means (e.g. reading in IMOD segmentation files) you can use that surface for masking instead of drawing it by hand.
(4) I don't understand the inverting problem so I couldn't say how to fix it, sorry. If possible, please explain it more or give a specific example to help us better understand.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 8, 2021, at 9:28 PM, 박시훈 via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear chimera-users community, I have questions about opening IMOD files in Chimera software. Can I open the IMOD files (*.mod) in Chimera? Or, Can I make a hand-drawn mask file in Chimera? I could apply several filters and masks in my iso-surface map, however, I don't know how to apply these options in Chimera. Moreover, the reconstructed tomograms were shown to the inverted iso-surface map unlike IMOD.. Can I re-invert the iso-surface map in Chimera?
Best regards Si Hoon Park
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